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Fig. 5 | BMC Bioinformatics

Fig. 5

From: CytoTree: an R/Bioconductor package for analysis and visualization of flow and mass cytometry data

Fig. 5

Analysis of time-course flow cytometry data reveals the induced differentiation process. a Experimental workflow and kinetics of CD43 and CD31 expression during the hematopoietic differentiation of HUES9 cells from D0 to D10. HUES9 cells were directionally differentiated into mesodermal cells (D4, cells with flattened shapes), hemogenic endothelium (D6, cells with squamous shapes) and HSPCs (cells in red) in succession. b UMAP visualization of the merged cells from the hematopoietic differentiation process. Cells are colored according to the time point from D0 to D10. c Construction of the hematopoietic differentiation trajectory based on UMAP coordinates using MST. d CD31, CD34, CD43, CD49f and CD90 expression markers are overlaid. e UMAP visualization of cells according to the hematopoietic differentiation process. Cells are colored according to the pseudotime. f Differentiation tree colored according to pseudotime. The cluster color is scaled to the mean value of the pseudotime for the cells within each cluster. g Density plot of the pseudotime for different differentiation days. h Heatmap of marker expression along with pseudotime progression. Each column represents a cell. The expression values are scaled by row and visualized using the z-score

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